To Hell and Back
by Kitsune1988
Summary: Elizabeth is attacked by the Genii during a routine mission. How will she get through this? Johns real feelings for Elizabeth come out. John/Weir whump.
1. Chapter 1

To hell and back

I don't know how or why, but this story plot randomly came into my head. I also have a few more SGA stories planned, including one real humour one! But no spoilers. You will see soon J

Weir is attacked by the Genii during a simple routine mission.

Disclaimer: I don't own SGA. All rights go to respectful and rightful parties.

May get minorly violent.

Sheppard/Weir whump

Chapter One

"When was the last time you came through the gate?" Colonel John Sheppard asked Dr Elizabeth Weir as they were checking out what appeared to be a recently abandoned village.

"Oh I don't know actually" she answered. "It feels good to actually get out for a change. To see what you guys get up to"

"Oh it can be boring, or interesting, or dangerous. Or annoying when Rodney gets into one of his moods" John said looking over at Rodney. Elizabeth couldn't help but smirk.

"Hey!" Rodney protested "I'm not that bad!"

"It looks like things didn't end well here, what do you think happened?" Teyla asked, taking in her surrounds

"I don't know, but I am starting to get a bad feeling, maybe we should-" Before John could finish his sentence, a herd of weapon fire started on them.

"Take cover!" Sheppard shouted as the team took shelter behind an abandoned house.

"Wait, that weapon fire looked awfully like….." Teyla started

"The Genii" Rodney finished her sentence.

Suddenly the team were surrounded by Genii solders, and John soon realised they were outnumbered.

They ceased fire, hoping that Ronan would sense something was wrong and come rescue them in the Jumper.

"Oh my, why would you look who it is" Said a familiar voice. John flinched; he knew exactly who this was. Kolya.

Kolya appeared before them all. "To what to we owe the pleasure?...As you can see, I did some redecorating" he said as we pointed to the ruins of a village.

"There were hundreds of people here, including children! What gives you the right to do this?! These people were kind people!" Teyla yelled as John and Elizabeth held her back.

"Well, I wanted the land, they said no, so I had to do something about it" Kolya replied with an evil grin.

Suddenly, weapon fire came from the sky. They all looked up to see the Jumper. Ronan. Unknown to the others, Teyla has quietly hit her radio and called Ronan who quickly came to their rescue. Everything went from 0 to 100 in a matter of seconds. Gunfire went off everywhere.

Ronan managed to distract the Genii solders while the team made a run for it to the Jumper. Ronan quickly landed the Jumper, Teyla and Rodney ran in.

"Where's Dr Weir and the Colonel?" Teyla asked, looking for them both.

She could see the Genii were moving in on them. "Get back to Atlantis and bring back a rescue team, and that's an order!" Elizabeth yelled and the solders surrounded them, outnumbering them by lots.

"But-" Rodney started

"GO!" John yelled

With that, Ronan shut the back door and got out of there as soon as he could.

"Ronan, we have to go back for them" Rodney pleaded

"You heard John and Weir, back to Atlantis and get a rescue team. We are outnumbered. We need reinforces

Ronan dialled the gate and went through the gate, parking the Jumper in the gate room.

"Ronan, where are Colonel Sheppard and Dr Weir?" Major Lorne asked as he approached Ronan.

"The Genii, we need to send a rescue team back, fast!" Rodney yelled.

With that, the rescue team was put into place.

Ooooooo

Meanwhile back at the planet, John and Elizabeth were taken hostage by the Genii and taking to a underground location.

"Your team won't find you here" Kolya said, happily.

John wanted to shoot him, then and there, but his weapons had been taken off him.

There were both thrown into a cell. Koyla entered the room with two armed guards.

"Now" Kolya asked "Which one of you is going to answer my questions?

Both Elizabeth and John remained silent, both refusing to answer any questions he asked.

"Cat got your tongue?" Kolya spat out. "Fine, if neither of you are willing to answer my questions, I will force them out of you. Elizabeth, you win the grand prize. You will be coming with me and will answer any questions I have"

"Never" Elizabeth shot back

"You leave her alone" John said through his teeth.

With that, Kolya nodded to both guards. One pinned John down and the other hit Elizabeth over the head and dragged her out of the cell.

"Elizabeth! Kolya, don't you DARE hurt her. Take me instead of her!" John yelled after Koyla, asked he and the guards left the room, one guard turning before locking the door and hitting John on the head with a gun, knocking Joh out cold.

OoooOooo

"Where are they?! There were right here! We dialled the gate as soon as we got back to Atlantis, there is no way the Genii would have made it on foot to the gate and dialled out" Rodney cried out.

He, Ronan, Carson and Lorne and his team had been searching for well over two hours, with no sign of Elizabeth or John anywhere. There wasn't even sign of the Genii. Just the mess they had left of the village.

"Those poor people" Carson said, looking very upset at what he was seeing.

"What, what is that?" one of Lorne's men said, pointing to an oddly looking patch on the ground. It looked very different to other parts of the planet. Lorne ordered a scan. "Looks like a door sir"

"Let's check it out" Lorne said. "But everyone, be careful."

With that, Ronan landed the Jumper, just next to the door and everyone excited the Jumper. Scanning above the door, Rodney exclaimed "I am reading both John and Elizabeth's signs! They are down there!"

From there, the team cautiously opened the door and ended. "You would have thought the Genii would have had this entrance more better guarded" Rodney whispered noticing the absence of guards.

OoooOoo

Meanwhile back in the cell, John started to wake up. His head hurt. Where was he? Oh right, John thought, a cell.

Suddenly, a rattle of a door caused him to turn around. A Genii guard threw a very badly beaten and unconscious Elizabeth into the cell and slammed the door behind him.

John ran over to her.

"Elizabeth! Can you hear me?" John cried out.

Elizabeth looked like hell. John felt her pulse. Very weak. "Oh please don't do this to me Elizabeth. You're going to be okay. We will be rescued; Carson will make you better and we will be okay. You hear me Liz?" John whispered to her.

True to his word, John heard lots of shouting and fighting beyond the door, then silence.

The door rattled, John moved in front of Elizabeth, ready to protect her from the Genii. But Ronan entered, along with the others.

"Thank god!" John yelled. "Carson, we need to get back to Atlantis. Elizabeth needs your help!

"Oh my god, Elizabeth?" Carson cried out while running to her and, at the look at her injuries. Everyone else was shocked.

John picked up Elizabeth and started running with the team back to the Jumper.

John was wondering what the Genii did to her, but he was soon to find out, and it was worse than any of them could have imagined.

TBC


	2. Chapter 2

_Thank you to those who have feedback and for the follows!_

To Hell and Back

Warning. Torture.

Chapter 2

"You will tell me what I want to know! Where is the coordinates of Earth? Who is your leader?! How do I get the ancient gene?!" Koyla yells

"Not very talkative?!"

Koyla burns Elizabeth with a soldering iron and orders his men to whip Elizabeth.

Beep, beep, beep. The sounds of beeps awaken Elizabeth from her flashbacks. Where was she? She opens her eyes, everything is bright and blurry. It takes her a moment to realise she is in the infirmary.

Suddenly she sees Koyla. Elizabeth pulls out her IVs and anything else attached to her tries to make a run for it.

"Whoa, Elizabeth! Where are you going?" Carson yells, suddenly appearing out of nowhere.

"It's Koyla, he's here! I need to get away from him." She says, pointing to where she had just seen him

Carson looks over in the direction Elizabeth was pointing. "There's no one there, you're hallucinating. You've been though a hell of a 24 hours. Please come back to bed" he responds, holding on to Elizabeth who can barely support her own weight under her.

"But he was right there, where did he go?" Elizabeth says, looking around the room.

Suddenly John appears in the room. "Elizabeth? He asks, looking concerned at how desperate Elizabeth looks. "What's going on?"

Carson leads her back into bed and puts her IV in. "She started hallucinating as she woke up. She said she could see Koyla"

"How are you feeling?" Carson asked, looking at her vitals as he helped ger back into bed.

"I've been better. John, how are you? Where did Koyla go? Is city safe? THE CITY!" Elizabeth cries out as she tries to get up and out of bed again, getting stopped buy Carson yet again with the help of John.

"John?" Elizabeth started.

"I am okay. Koyla, he got away on the planet but as soon as I get my hands on him…" John started, sounding her angry.

"Hold it Coronel. Elizabeth, what do you remember?" Carson asked, as he finished listening to her breathing with a stethoscope

"I remember a room, some dungeon of some sort. He asked so many questions, I wouldn't answer him so her tortured me. I don't remember much, I'm sorry "

"Aye, don't be sorry. You have signs of trauma to parts several parts of your body including your head, so the memory loss is not unusual. I suspect you will get your memory back as you progress. But I am taking you off duty and keeping you here in the infirmary for an unknown time, It depends on your recovery. You have several cracked ribs, a concussion bruising, concussion and burns. And that is just for starters. There are other cuts and graziers on you too." Carson started. He could see Elizabeth tearing up.

He took her hand. "The best you can do now is rest, let your body heal. And I recommend you talk to Dr Heightmeyer. I suspect you have been through a lot. And there is going to be emotional trauma."

Elizabeth wasn't exactly happy about having an upgrade from her quarters to the infirmary for an extended stay. She hated the infirmary as much as John did.

"But'-" Elizabeth started.

"No buts, or I will pull medical rank on you" Carson started.

"Listen to the nice doctor" John said, smirking. Elizabeth didn't see him smirking, but Carson did.

"You're not a good role model when it comes to staying in bed, Colonel" Carson said, rolling his eyes.

Elizabeth was too exhausted to fight Carson anymore, she looked at John who nodded and closed her eyes and let sleep come at her.

John patted her hand softly and left the room with Carson.

"Doc? How is she really?" John asked, feeling as if Carson was keeping something from them both.

"She's been through a lot. She is showing signs of severe torture. While her body may heal, it's the mental recovery that is going to be the hardest. It's not going to be a walk in the park. I don't know how she is going to react from what she has gone through. Especially once she starts remembering what happened to her." We won't know exactly what she has been through apart from looking at her injuries and making assumptions. However, there is some odd marks on her forehead. I remember reading about this in some medical files from the SGC. It looks like some sort of memory recall device." Carson replied, his voice starting to break. It broke his heart to see someone who he admired and cared about, look so hurt and helpless.

"Colonel, where are you going?" Carson asked, watching John storm away

"To teach that Koyla guy a lesson!" he yelled, as he disappeared down the hall.

"Colonel, you should be resting, you got hurt too, you know!" Carson yelled at him, hoping he could hear, but fighting doubting it. He knew there was no fighting him right now. He just hoped John would be careful, whatever his plans could be

OoooOoo

"Please tell me you have good news" John asks Lorne and his team, as they arrived back. Some of the rescue team had remained on the planet to try to find any survivors from the initial village.

"The Genii are gone. There is no trace of any of them, including Koyla. But there is one thing." Lorne began. "The underground where we found you and Elizabeth, we found the room where we think she was taken. But it was different to everywhere else. It gave off strange energy readings. It seems to be some sort of time dilation device. If our scans are correct, 2 hours in the room was equivalent to around 72 hours in the room…"

"So, what you're are telling me, that while we initially thought Elizabeth was held captive for about 24 hours with the freak, she was actually held for 72 hours?" John started, trying to keep his voice calm.

"Yes"

John stormed back to the infirmary and sat down next to Elizabeth. "Don't worry Liz, we will get him. And you will get through this, okay? I can't run the city alone, and please don't make me have to deal with Rodney alone"

Elizabeth opened her eyes. "John?"

"Oh hey Liz. Howe are you feeling?"

"Super…. thirsty actually" she replied, starting to reach for the water in front of her.

John picked up the jug of water, filled the cup, put a straw in it, and handed it to Elizabeth, helping her drink.

"Thanks" she smiled. "John, please don't beat yourself up over this. This was not your fault. He tried to get information out of me about Atlantis and Earth. But I refused, so he hurt me, a lot. He then put some mind thing on me, and I am quite sure he got the information he needed. I'm sorry…..oh my god, Earth! I need to inform the SGC" Elizabeth said, starting to get shaky and attempting to get out of bed.

"Hey, hey, hey, Liz just stay in bed, you let us deal with that" John said, locking her from getting out of bed, along with Carson.

"Carson, where did you come from?" John asked, noting his sudden appearance.

"Elizabeth, good to see you awake. How are you feeling?" Carson replied, ignoring John's question.

"I could be better, I feel dizzy and I hurt everywhere, my head is also thumping." Elizabeth replied, rubbing her head.

"Aye, that is excepted. Coronel, would you mind giving me a little time? I would like to have a chat with Elizabeth and run a few scans." Carson said, as he ushered John out of the infirmary.

Carson ran the usual scans, took Elizabeth's vitals and some bloods, all while looking at her in sympathy.

He left her alone while requesting her to get more sleep and went into her office, almost running into John.

"Have you been there the whole time? I thought I told you to go away!" Carson said in annoyance.

"You said you wanted some time alone with Elizabeth, you didn't say go away….how is he?"

Carson sighed. "No different to how she was when she arrived. How she is actually awake and talking with her injuries, amazes me, technically, she should be dead. She is the strongest woman I know.",

Meanwhile, Elizabeth layed in bed, her back facing Carson and John. Little did they both know, she could hear them both, word for word. As she lay, thinking about what she had gone through, she saw Koyla run pass the door of the infirmary. She turned around, and saw Carson and John still talking. She made a run for it, regardless of how dizzy and the pain she felt when moving.

"Lorne to Sheppard." John heard on his radio

"Go ahead Major"

"We have a problem. We have had a few reports of others seeing Koyla around the base" Lorne said

John and Carson looked at each other

"So, either more people are hallucinating or…" Carson began

"Koyla is here at Atlantis" John said.

TBC


	3. Chapter 3

Thanks for the reviews!

Rated T

(Third attempt at uploading this story, getting some weird error messages when it posts and the words are all computer code. Yeah I don't know what happened either!)-_-*

Chapter 3

Elizabeth ran towards the weapons locker. She saw two guards outside the room, guarding and also chatting at the same time. She pulled a hair pin out hair and threw it, hiding behind a wall as she did. She peaked through a gap and watched the guards go to investigate and she ran into to the room, grabbed what she could to defend herself, then ran out. Elizabeth noted she needs to tell the security team how easy it was to get in and out of the weapons locker undetected.

Suddenly, WHAM! Elizabeth was pushed to the ground then picked up by the scruff of her top.

"Well, well, well. Would you look who it is, look what the cat bought in?" Koyla said. "Now, come with me"

Koyla started dragging her, keeping a knife close to her neck.

"Where are you taking me? You won't get away with this!" Elizabeth protested. The adrenaline was already starting to ware off, and started to feel too weak to fight him.

"We're going to take a Jumper, return to my new planet and go my lab, where you will help me build what I ask with your Earth scientific secrets"

"Wait, WHAT?! What could you possibly, know about Earth?" Elizabeth asked annoyed and shocked.

"Oh yes, you don't remember" Koyla chucked "I used a mind probe on you. I know all about Earth!"

Elizabeth cringed. He was right. The probe was able to get many thoughts, even supressed thoughts.

"You won't get through the gate alive. They won't allow it. I will sacrifice myself before you get out of here!" Elizabeth yelled and tried to get out of his grip, but it was no use, he was too strong, and she wasn't strong enough.

Koyla dragged Elizabeth up to the Jumper bay and pulled Elizabeth into a Jumper, closed the Jumper bay doors and started flying the Jumper towards the gate room. Since when was Koyla able to fly a Jumper? Didn't he need an ancient gene to fly it? Elizabeth found herself wondering.

"Uh, Sir, the gate just activated" Chuck said, confused

John turned around only to see the Jumper descend from the Jumper bay, and towards the gate. "Activate the shield" Chuck activated the shield "Koyla? Let Elizabeth go, let's talk through this" John said, trying to keep his voice calm and low, John could feel his blood starting to boil.

Koyla ignored him, somehow over righted the shield and went through the gate.

John quickly noted the gate address and summoned his team, as well as extra security personal. He wasn't going to let Koyla get away with this. He promised himself he will bring Elizabeth back to Atlantis.

"Chuck, dial the gate"

OoooOoo

As soon as Koyla and Elizabeth arrived at the planet, Koyla redialled the gate to another planet. "Let's see if your little teammates can find you now!"

Little did Koyla know, or at least Elizabeth hoped he didn't know from the mind probe, that they had technology that would track the addresses each gate had dialled.

They both arrived at another planet, Elizabeth quickly realised this planet didn't originally belong to the Genii, so they most definitely stole it from another civilisation.

Koyla stopped at an underground location. Elizabeth took in her surroundings, then everything went black.

Back on the original planet, John was starting to pull his hair out. "Where the hell are, they?! They couldn't have gone far!"

John was clearly annoyed. They have scouted the planet for hours, and there was no signs of Elizabeth or Koyla.

"Is it possible they have dialled to another planet?" Teyla asked

John paused, yes possibly. "Rodney, do you remember how to access the gate's addresses?" John asked hopefully. John remembered that SG1 had used it before and he hoped Rodney knew how.

"Yeah I should be able to do that. It's definitely worth a try." Rodney said as John landed the Jumper in front of the gate. John knew it was a long shot, anyone could have used the gate and he knew the chances of the recent dialled planet being the one Koyla and Elizabeth were was slim, but what did they have to lose?

"Okay, got it" Rodney said. John ordered Rodney to dial the planet, which Rodney did in a heart beat.

OooOo

Elizabeth opened her eyes, feeling quiet disorientated, it took her a minute to realise she was tied to a chair. She tried to pull herself free, but the restraints were too strong.

"Look who finally woke up"

Elizabeth looked up and saw Koyla.

"Now, are you going to be a good girl and help me, or do I need to you this one you?" Koyla held up a mind probe "Upgraded version, and if you don't help me, I use it on you to implant memories into your mind, that you won't know what is real or not, and you won't like it."

Elizabeth shook her head and looked away.

"Fine, you give me no choice."

Koyla stepped forward and despite Elizabeth's protests, put the probe on her, biting him in the process.

Elizabeth immediately started to see visions, Koyla's visions, Wraith visions and Genii visions.

Elizabeth started to feel all feelings, anger, scared, and she started to find it difficult to what was real and what was not real.

Koyla was right.

John, Rodney, Teyla, Ronan, Lorne, Carson and a few marines, circulated the planet until Rodney picked up an unusual energy reading.

"I'm reading a lifeline! It's Elizabeth's!"

John couldn't believe their luck, they found her.

John quickly landed the Jumper and the team started to run downstairs to a long hall.

"Okay, take it easy, use any necessary force, but do not, I repeat, do not hurt Elizabeth" John whispered.

"You really need to warn us not to hurt her? Rodney shot back.

The team ran down the halls, knocking out any guards until they came to a closed room. They could hear Koyla's shouts and Elizabeth's protests.

John ran in, the team following.

"Oh look, your little play mates!" Koyla said, unknownly knowing Roman had slipped behind him.

"So, your leader here, refused to help me, again, but don't worry, I took care of her, she-" Koyla fell in his tracks as Ronan stunned him.

John and Carson ran towards Elizabeth. Carson checked for a pulse while John and Ronan freed her from the restraints.

"We need to get her back to Atlantis, NOW" Carson said, noting her faint pulse and the general look at her injuries.

"Dammit, Liz, what did that monster do to you?" John whispered to Elizabeth as he helped Ronan carry Elizabeth carefully into a Jumper and place her on the ground.

Carson quickly started to take any vitals he could without his usual medical machinery as John watched helplessly and Rodney started the Jumper up and made their way back to the gate.

"She's struggling to breath" Carson signed, as he listened to Elizabeth's breathing with a stethoscope.

"Rodney, how much longer, I can't treat her well enough without medical equipment" Carson said

"I'm going as fast as I can!" Rodney yelled back, but quickly sighed a breath of relief when he sighted the gate. "Okay, dialling the gate! Ronan, enter your IDC"

"It's okay Liz, we're nearly back at Atlantis, please don't do this again to me, we need you. I can't run this place as well as you do"

The Jumper arrived at Atlantis, and Rodney guided the it to the Jumper bay. A medical team was waiting for them. Carson started barking out orders, as the medical team followed suit. John, Rodney, Ronan and Teyla watched on, everything felt as if it was in slow motion. John stepped forward, only to have Carson stop him. "Not now Colonel, I need to get her to the infirmary. I will keep you posted; I promise"


End file.
